Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome

Transcriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related to environmental stress and plant-pathogen interaction. Currently, next generation sequencing platforms are used to obtain a high amount of raw data to build the transcriptome of any plant. Here, we compare Illumina and Ion Torrent sequencing platforms for the construction and analysis of the holm oak (Quercus ilex) transcriptome. Genomic analysis of this forest tree species is a major challenge considering its recalcitrant character and the absence of previous molecular studies. In this study, Quercus ilex raw sequencing reads were obtained from Illumina and Ion Torrent and assembled by three different algorithms, MIRA, RAY and TRINITY. A hybrid transcriptome combining both sequencing technologies was also obtained in this study. The RAY-hybrid assembly generated the most complete transcriptome (1,116 complete sequences of which 1,085 were single copy) with a E90N50 of 1,122 bp. The MIRAIllumina and TRINITY-Ion Torrent assemblies annotated the highest number of total transcripts (62,628 and 74,058 respectively). MIRA-Ion Torrent showed the highest number of shared sequences (84.8%) with the oak transcriptome. All the assembled transcripts from the hybrid transcriptome were annotated with gene ontology grouping them in terms of biological processes, molecular functions and cellular components. In addition, an in silico proteomic analysis was carried out using the translated assemblies as databases. Those from Ion Torrent showed more proteins compared to the Illumina and hybrid assemblies. This new generated transcriptome represents a valuable tool to conduct differential gene expression studies in response to biotic and abiotic stresses and to assist and validate the ongoing Q. ilex whole genome sequencing

Development of New Antiproliferative Compound against Human Tumor Cells from the Marine Microalgae Nannochloropsis gaditana by Applied Proteomics

Proteomics is a crucial tool for unravelling the molecular dynamics of essential biological processes, becoming a pivotal technique for basic and applied research. Diverse bioinformatic tools are required to manage and explore the huge amount of information obtained from a single proteomics experiment. Thus, functional annotation and protein-protein interactions are evaluated in depth leading to the biological conclusions that best fit the proteomic response in the system under study. To gain insight into potential applications of the identified proteins, a novel approach named "Applied Proteomics" has been developed by comparing the obtained protein information with the existing patents database. The development of massive sequencing technology and mass spectrometry (MS/MS) improvements has allowed the application of proteomics nonmodel microorganisms, which have been deeply described as a novel source of metabolites. Between them, Nannochloropsis gaditana has been pointed out as an alternative source of biomolecules. Recently, our research group has reported the first complete proteome analysis of this microalga, which was analysed using the applied proteomics concept with the identification of 488 proteins with potential industrial applications. To validate our approach, we selected the UCA01 protein from the prohibitin family. The recombinant version of this protein showed antiproliferative activity against two tumor cell lines, Caco2 (colon adenocarcinoma) and HepG-2 (hepatocellular carcinoma), proving that proteome data have been transformed into relevant biotechnological information. From Nannochloropsis gaditana has been developed a new tool against cancer-the protein named UCA01. This protein has selective effects inhibiting the growth of tumor cells, but does not show any effect on control cells. This approach describes the first practical approach to transform proteome information in a potential industrial application, named "applied proteomics". It is based on a novel bioalgorithm, which is able to identify proteins with potential industrial applications. From hundreds of proteins described in the proteome of N. gaditana, the bioalgorithm identified over 400 proteins with potential uses; one of them was selected as UCA01, "in vitro" and its potential was demonstrated against cancer. This approach has great potential, but the applications are potentially numerous and undefined

Consens d’escales i eines per a la valoració multidimensional de les persones a Catalunya

Model d'atenció integral; Valoració multidimensional; DiagnòsticModelo de atención integral; Valoración multidimensional; DiagnósticoComprehensive care model; Multidimensional valuation; DiagnosisActualment no existeix a Catalunya un consens sobre quin hauria de ser el mínim comú denominador d’escales i eines d’elecció per a la valoració de les diferents dimensions de les persones grans amb multimorbiditat, fragilitat, cronicitat complexa o avançada. Aquest escenari fa evident la necessitat de disposar d’escales i eines consensuades i compartides que facilitin l’aproximació multidimensional a aquestes persones de forma objectiva i pragmàtica, amb l’objectiu d'ajudar els professionals en aquest procés d’individualització de l’atenció. És per aquest motiu que, impulsat per la Direcció General de Planificació i Recerca en Salut i per l’oficina eSalut, s’ha promogut i desenvolupat aquest consens i es vol assegurar que la proposta pugui ser suportada en l’entorn digital

Comparative proteomic analysis of Arabidopsis wild-type, mutants, and Fa WRKY1 transgenic plant to characterize the function fo strawberry (Fragaria X ananassa) Fa WRKY1 protein and its Arabidopsis homolog, at WRKY75 two positive regulators of resistance

Comunicaciones a congreso

Identification and validation of reference genes for transcript normalization in strawberry (Fragaria × ananassa) defense responses.

Strawberry (Fragaria spp) is an emerging model for the development of basic genomics and recombinant DNA studies among rosaceous crops. Functional genomic and molecular studies involve relative quantification of gene expression under experimental conditions of interest. Accuracy and reliability are dependent upon the choice of an optimal reference control transcript. There is no information available on validated endogenous reference genes for use in studies testing strawberry-pathogen interactions. Thirteen potential pre-selected strawberry reference genes were tested against different tissues, strawberry cultivars, biotic stresses, ripening and senescent conditions, and SA/JA treatments. Evaluation of reference candidate's suitability was analyzed by five different methodologies, and information was merged to identify best reference transcripts. A combination of all five methods was used for selective classification of reference genes. The resulting superior reference genes, FaRIB413, FaACTIN, FaEF1α and FaGAPDH2 are strongly recommended as control genes for relative quantification of gene expression in strawberry. This report constitutes the first systematic study to identify and validate optimal reference genes for accurate normalization of gene expression in strawberry plant defense response studies

Proteomic approach to the bioluminescent dinoflagellate Pyrocystislunula

Trabajo presentado en las V Jornadas de Jóvenes Investigadores en Proteómica, celebradas en Toledo el 19 y 20 de junio de 2017.Some living organisms are able to produce light by a chemical reaction in a process named bioluminescence. This capacity is widely distributed in all organisms appearing in insects, microorganism, fungi, etc. In spite of minor differences, all bioluminiscentorganism based this process in the interaction of the substrate luciferin with the enzyme luciferase. Recently, bioluminescence is being applied to different biotechnology procedures. P. lunula is a bioluminiscent Dinoflagellate with crescent-shaped cell morphology of 0.15 mm in length. During the night, cells produce blue light when shaken or disturbed. Due to the great potential for biotechnology innovation that is present in seas and oceans, we select this microalgae to explore it protein content looking for new pharmaceuticals or industrial products. In addition, we expect go into the bioluminescent process of this organism exploring its potent biotechnological applications. Flask containing P. lunula samples were cultured in L1 medium under 12h photoperiod at 22°C. Protein extracts were obtained by Phenol-TCA-Acetone based method. Tryptic protein peptides were identified by LC-MS. Due to the lack of molecular information of this microorganism, transcriptome database was generated. This is the first approach to the proteome of P. lunula. Identified proteins has been discussed above it role in the bioluminiscent process and its potential use in agrifood and/or biomedicine.N